xVolcano: Function to draw a volcano plot

Description Usage Arguments Value Note See Also Examples

View source: R/xVolcano.r

Description

xVolcano is supposed to draw a volcano plot

Usage

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xVolcano(data, column.lfc = "lfc", column.fdr = "fdr",
cutoff.lfc = 1, cutoff.fdr = 0.05, colors = c("#EEEEEE",
"darkgrey", "pink", "red"), column.label = NULL, top = 10,
top.direction = c("both", "up", "down"), label.size = 2,
label.color = "black", label.alpha = 0.8, label.padding = 0.5,
label.arrow = 0.01, label.force = 0.5, xlim = NULL, ylim = NULL,
y.scale = c("normal", "log"),
xlab = expression(log[2]("fold change")),
ylab = expression(-log[10]("FDR")), font.family = "sans",
signature = TRUE)

Arguments

data

a data frame

column.lfc

a character specifying 'lfc' column (log2-transformed fold change)

column.fdr

a character specifying 'fdr' column

cutoff.lfc

a numeric defining 'lfc' cutoff. By default, it is 1 (at least 2-fold changes)

cutoff.fdr

a numeric defining 'fdr' cutoff. By default, it is 0.05

colors

a 4-element vector for color-coded points. By default, it is c("#EEEEEE","darkgrey","pink","red")

column.label

a character specifying 'label' column

top

an integer specifying the number of the top points for labellings

top.direction

the direction (up- and down-regulated) of the top points. It can be one of 'both' (up- and down-regulated), 'up' (up-regulated only) and 'down' (down-regulated only)

label.size

the label size

label.color

the label color

label.alpha

the 0-1 value specifying transparency of labelling

label.padding

the padding around the labeled

label.arrow

the arrow pointing to the labeled

label.force

the repelling force between overlapping labels

xlim

the limits in the x-axis

ylim

the limits in the y-axis

y.scale

how to transform the y scale. It can be "normal" for no transformation, and "log" for log-based transformation

xlab

the x labelling. By default, it is expression(log[2]("fold change"))

ylab

the y labelling. By default, it is expression(-log[10]("FDR"))

font.family

the font family for texts

signature

logical to indicate whether the signature is assigned to the plot caption. By default, it sets TRUE

Value

a ggplot object

Note

none

See Also

xVolcano

Examples

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## Not run: 
# Load the library
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

## End(Not run)

hfang-bristol/XGR documentation built on Nov. 18, 2018, 2:37 a.m.